Metagenome analysis of pig nasal swab samples by Oxford Nanopore and Illumina sequencing

Abstract

Our study delved into the microbial community dynamics and antibiotic resistance gene profiles within swine samples utilizing Illumina and Oxford Nanopore Technologies sequencing methods. Eukaryota dominated all samples, followed by Bacteria. The detection of 22 bacterial genera, each varying in abundance across different ages, underscores the potential impact of genetic factors, environmental conditions, and antibiotic exposure on microbial diversity. The detection of 18 resistance genes highlighted the concerning prevalence of antibiotic resistance within swine populations. Aminoglycoside resistance genes, particularly AAC(6')-I43 and AAC(6')-Il, were prevalent, suggesting a potential role in resistance transmission. The presence of ANT(3'')-IIa and APH(3')-Ia genes underscored the diversity of resistance mechanisms against streptomycin and spectinomycin.